Project Summary The Functional Genomics and Microbiome Core (Core C) supports the mission of the DDC and enhances research programs in its theme of infection and injury affecting the mammalian intestine and liver. We continue to enhance the scope of the Core, based on DDC user demand and our firm commitment to the importance of the microbiome in gastrointestinal and liver biology. The emphasis of this Core is on functional genomics and how genes present in the mammalian microbiome and in mouse/human genomes may yield functional RNAs, proteins and metabolites that help stitch together a deeper and mechanistic understanding of digestive diseases. Our mission is to provide a full-service resource from experimental design to consultations about specimen processing, robust data analysis pipelines, bioinformatics strategies, and biostatistical support. In summary, we have created a fully integrated genomic and multi-`omic analysis platform for investigators studying digestive diseases. This Core serves DDC investigators by providing expertise in microbial and mammalian genomics, transcriptomics, metabolomics and protein analytics, as applied to gastrointestinal infection and injury states. Research programs nurtured by DDC members are facilitated by this Core's ability to bridge microbiome science and mammalian biology, and to provide multi-tiered services at the levels of genes and effectors (proteins and metabolites). This Core deploys the tools/services of microarrays, deep nucleic acid sequencing (microbial and mammalian), protein multiplexing, mass spectrometry-guided metabolomics, and bioinformatics. PCR-based analyses of gene expression and splicing, DNA mutation/SNP detection, and gene pathway analyses of the mammalian metagenome (microbe and man) will be fostered by this Core as a platform for gastrointestinal and hepatic systems biology. This Core presents a combination of shared as well as exclusive offerings to TMC DDC members. The Microbiome and Mammalian Genomics services provide valuable capital-intensive resources shared among DDC and non-DDC members at BCM. DDC members account for about 10% of institutional usage of metagenomics and mammalian genomics services. The Metabolomics/Mass Spectrometry, Protein Multiplexing, and Bioinformatics services are TMC DDC member-exclusive services, not offered to non-DDC members as Core functions.